how to get noncoding RNA sequence
Shiaoching Gong
Dear Sir/Madam,
Good morning.
I am searching a list of non coding RNA in human 6q23 locus from UCSC. I typed gene names of TNFAIP3, clicked Genes and Gene Prediction Tracks and selected for Gencode, but could not find the list of non coding RNA around the region.
Could you please let me know how to see the list of noncoding RNA and how to get the sequence of them?
Thank you very much,
Shiaoching Gong
Jonathan Casper
Hello Shiaoching,
Thank you for your question on obtaining sequence for non-coding regions. The short answer is that you should be able to find a list of non-coding elements in the region by applying a filter to your query where cdsStart=cdsEnd. Since you specifically mentioned the Gencode track, I'll provide instructions for working with that.
1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables, also accessible by clicking "Table Browser" from the left navigation bar on our homepage at http://genome.ucsc.edu
2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: GENCODE Genes V14
Table: Basic (wgEncodeGencodeBasicV14)
For this example, we'll use the Basic table. For descriptions of the other options, see the track details page for Gencode V14 (visible by clicking the Gencode supertrack on our main browser page at http://genome.ucsc.edu/cgi-bin/hgTracks, then clicking on the V14 subtrack).
Region: position, enter in "6q23", and click "lookup".
For this example we will look at your 6q23 location. You can also enter a specific gene identifier here.
Output format: Sequence
3. On the "filter" line, click the "create" button
4. In the "Filter on Fields from hg19.wgEncodeGencodeBasicV14" section, enter the following in the "Free-form query" box: cdsStart=cdsEnd
5. Click the "submit" button
6. Click the "get output" button
7. Leave "genomic" selected and click "submit"
8. Configure the sequence display as desired and click the "get output" button
Please note that this search depends on a fairly simple definition of non-coding region (cdsStart=cdsEnd). You can use the following steps 4a and 4b (replacing step 4) to create a more restrictive filter that omits the Gencode biotypes retained_intron, TEC, and disrupted_domain (see http://www.gencodegenes.org/gencode_biotypes.html for more information).
4a. Under "Linked Tables", check the box next to wgEncodeGencodeAttrsV14 and click "allow filtering using fields in checked tables".
4b. Under hg19.wgEncodeGencodeAttrsV14 based filters, set transcriptClass DOES match "nonCoding".
For more information on this topic, you may wish to search our mailing list archives (accessible by clicking "Contact Us" from the left navigation bar of our main page at http://genome.ucsc.edu). The answer to this question in particular may also be useful.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Staff
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